I do see backups in my tmp directory. But they do not appear large enough either.
I believe someone may have gotten access to the system and wiped out the databases, before I ran the upgrade.
With the assumption I do not have a database backup.

Can I recreate the hosts and users and be OK as long as the hosts are in the right order?

What happened was I was doing the update via ssh, and I got preoccupied with something else, When I came back my session had timed out but it was to the point where it asked me for an email address for ISPConfig to use. I went back and tried to re-run the install but as soon as I noticed this was for a fresh install I canceled out.

The last backup of the ful database was last night with no changes made since then other than running the upgrade script. What is the best way for me to proceed?

Shutting down ISPConfig system...
/root/ispconfig/httpd/bin/apachectl stop: httpd (no pid file) not running
ISPConfig system stopped!
Starting ISPConfig system...
/root/ispconfig/httpd/bin/apachectl startssl: httpd could not be started
ISPConfig system is now up and running!
Congratulations! Your ISPConfig system is now installed. If you had to install quota, please take the steps described in the installation manual. Otherwise your system is now available without reboot.

but I am unable to access the admin page. Any help on where to look to fix this would be much appreciated. Oh and it never asked me for an email this time.

Well... I've been trying everything I can think of to get this working. After much searching, I am still at a loss. I can run apachectl start and then I can access the ISPConfig admin page at a http://xx.xxx.xxx.xxx:81 but there are a lot of errors. When I try apachectl startssl I get the same message as above "httpd could not be started" Any ideas on where to focus my efforts would be much appreciated.

Ahhhh... I screwed it up... I had gone to try the update one more time like you had suggested earlier Till and this time while it's checking files I get a ton of errors like these:

openssl-0.9.8d/VMS/ucx_shr_decc.opt
tar: openssl-0.9.8d/VMS/ucx_shr_decc.opt: Cannot open: No such file or directory
tar: Skipping to next header
openssl-0.9.8d/VMS/ucx_shr_vaxc.opt
tar: openssl-0.9.8d/VMS/ucx_shr_vaxc.opt: Cannot open: No such file or directory
tar: Skipping to next header
openssl-0.9.8d/VMS/VMSify-conf.pl
tar: openssl-0.9.8d/VMS/VMSify-conf.pl: Cannot open: No such file or directory
tar: Skipping to next header
openssl-0.9.8d/VMS/WISHLIST.TXT
tar: openssl-0.9.8d/VMS/WISHLIST.TXT: Cannot open: No such file or directory
tar: Skipping to next header
tar: Error exit delayed from previous errors

Click to expand...

for what looks like every file and then it ends with

ERROR: Could not unpack OpenSSL
cd: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
mv: cannot stat `binaries/aps.tar.gz': No such file or directory
mv: cannot stat `binaries/spamassassin.tar.gz': No such file or directory
mv: cannot stat `binaries/uudeview.tar.gz': No such file or directory
mv: cannot stat `binaries/clamav.tar.gz': No such file or directory
mv: cannot stat `binaries/cronolog': No such file or directory
mv: cannot stat `binaries/cronosplit': No such file or directory
mv: cannot stat `binaries/ispconfig_tcpserver': No such file or directory
mv: cannot stat `binaries/zip': No such file or directory
mv: cannot stat `binaries/unzip': No such file or directory
tar: spamassassin.tar.gz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
mv: cannot stat `spamassassin': No such file or directory
tar: uudeview.tar.gz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
mv: cannot stat `uudeview': No such file or directory
tar: clamav.tar.gz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
mv: cannot stat `clamav': No such file or directory
tar: aps.tar.gz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
./setup2: line 860: ispconfig_tmp/php/bin/php: No such file or directory
ERROR: The PHP binary coming with ISPConfig does not work properly on your system! The installation routine stops here!

Click to expand...

I'm not going to touch anything else until I hear back. Am I to the point where I need to do a fresh install of ISPConfig? And if so, is there a topic anywhere about restoring a backup onto a fresh install? I haven't seen one yet.

Do the directories /root/ispconfig and /home/admispconfig and the ISPConfig database exist? If not, check your /tmp directory, there should be backups of both directories and a dump of the ISPConfig database from which you can restore your previous installation.

I have copied the 3 files to a different hard drive and cleared out some more space on the root. Then I'm going to untar the backup to /root/ispconfig Is this the right course of action with this?

EDIT: I Found the culprit... 4 months of daily database backups in the 300MB range each... they should be going to my backup hard drive, but for some reason they are on the root... I'll have to change that.